One year on

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This time last year, I was a newly-minted PhD, still revising my dissertation. I had just accepted my job at Briggs, and I was preparing for a conference, a vacation, and a new routine.

I don't remember much of my defense. My parents came to see it, even though it was a Wednesday afternoon and a 10-hour drive from their home. I was sleep-deprived and panicky. I couldn't remember the order of my slides, even though I'd given many variations of that same talk all the way through grad school. When I finished my talk, I cried.

My defense wasn't advertised beyond a poster on the seminar board alongside a dozen other defenses scheduled for the same week. Besides my committee and labmates, almost no one came. I'd been a bit disappointed about this when I started, but that turned to relief and gratitude when I was dabbing my eyes and pulling myself together most of an hour later.

I don't remember what questions the audience asked, and only one of the questions from my committee afterward. One committee member asked for a set of values in a tone of voice that, to me, implied I hadn't done my due diligence. Seeing as that value was highlighted in a table, sleep-deprived me lost patience and told said committee member to read the dissertation. I think I said something like "you'll find that on page 47 in table 2.3," but my internal dialogue was closer to "you obviously didn't bother to read my dissertation," so it's entirely possible that I said something else.

We celebrated in a conference room around the corner from my lab office. My labmates made me a goofy paper hat decorated with pictures of things they associated with me. It was very sweet of them, and moreso because it was a surprise. The hat is now a lab tradition, and I hope it continues. I am Graduate #1. I got to see the start of a lot of lab traditions.

I turned in my dissertation a month later, and continued to work in the lab, wrapping up projects and working on a collaboration up until I left for the conference (and subsequent vacation) in Europe. When I got back, everything was different.

I started at Lyman Briggs College in August.1 It was a new job at a new place, with new colleagues and new students, and I had to learn everything. Where is the copier? What are the college policies? Who do I ask for X or Y? Where to I park my car? What order will we cover the course material in? How deep do we dive into each chapter? How does the course website work? What resources are available? And on and on and on. An overwhelming amount of newness in my environment and also in what was expected of me.

It took me most of the fall semester to get used to being a professor. Some aspects, like delivering lectures, holding office hours, and making copies were familiar. But others -- being the authority the learning assistants turned to, handling grade disputes, offering feedback to colleagues with much more experience than myself -- took a big shift in mindset.

I have learned a lot in the past year. No longer a student, but an instructor, still I continue to grow and learn. Last year, I'd made and given a small handful of lectures. One year on, I've not just delivered 120 lectures to hundreds of students, I've also kept up the routine. When you're a grad student interviewing for a job, you can refine a teaching demo over the course of a week or more. When you're teaching, one awesome talk on Monday is not enough. You've got to be ready for class on Wednesday and Friday as well.

Academia is a flexible place to work. I can grade in my office or at home. I can decide to eat lunch with a friend near home, rather than spending a day on campus. Inspirations for lecture and practice problems can come form anywhere. But academia is also a rigid place to work. When I have a lecture, I must be there. I can't reschedule it. One hundred twenty-five students will be there, whether I am or not. One year on, I'm still getting the hang of this combination of rigidly structured and fully unstructured time.

When I started at Briggs, few people had seriously called me "Dr. Haas." It took a while to get used to; not just the title change (thought it was a much faster transition than when I changed my name after marriage), but the notion that I was a doctor of some sort. I couldn't tell my students to go ask their professor -- that professor was me!

I'd look at Facebook and see friends from high school, college and my time as an exchange student, and I'd see the great things they'd done, places they'd gone, children they'd had, careers they'd built, and I'd think "What have I done with my life?" And then my husband would point out that none of the people in question had doctorates in chemistry, that I'd spent five years in pursuit of that degree, and that I should very much give myself a break.

You see, despite five years of graduate school and all it entailed, it was (and sometimes still is) easy to forget I'd actually gotten a PhD. It's my own flavor of Impostor Syndrome, I guess. That nagging feeling that there'd been some mistake. That I wasn't really good enough for a PhD from a highly ranked university. That they gave me a PhD to get rid of me because they pitied me, but I'd gotten too far for them to kick me out.

One year on, I answer to "Dr. Haas," "Doc," "Professor," and occassionally "Prof Haas" without blinking. I've stopped feeling like the mail room is off-limits, or like I'm a child in an adults-only space. I am less surprised when a colleague asks for my input or feedback.

When I started I feared for the way I'd measure up to stereotypes. I dressed up a little; I wore khakis and slacks. I addressed emails to students more formally than my usual style. I checked and double-checked my work for errors so my students wouldn't see me fail.

One year on, I'm in skirts every Friday. It started as "Formal Fridays" in my mind, but soon became "Fearless Fridays" when I discovered that dressing like myself gave me a confidence boost. I can tackle so much more in my dress boots and a skirt than in my fall semester "uniform."

One year on, I still make mistakes. Having yet to achieve apotheosis, I expect the mistakes will continue. ;-) But I'm learning. I make new and different mistakes, and my ability to make corrections -- and let the students and learning assistants correct me -- can be evidence to my students that you don't have to be right all the time. When it comes to dealing with students, I've relaxed.

Last year my colleagues were strangers. My freshmen hadn't yet graduated high school. I had a plan for only one year. One year on, my colleagues are mentors and friends, my students have settled into college life, and my one-year job is at an end.

It has been a real delight to work at Briggs with such wonderful, supportive, creative faculty (and staff!) and highly motivated students. The students may not all love chemistry, but they do see the value in it. They challenge me and surprise me. They are funny and insightful and earnest. They bring me so much joy. I am sad to go.

But I won't be sad forever. This spring I accepted a tenure-stream position at Misericorida University. I have new colleagues, new students and a new plan. I'm thrilled, even as I start to take farewell of Briggs and MSU. I have more to learn, more ways to grow, and another good place to do it.

So here's to another year. Wish me luck.

1: Lyman Briggs College (aka Briggs) is a residential science college at Michigan State University: all of the students are science majors of one sort or another. In addition to taking intensive, group-focused introductory science and math courses together, the students also take courses on the history, philosophy and sociology (aka HPS) of science. It's a pretty cool place to work, and I'd have loved it as a student there.

The Invisible Woman

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I wrote this in October and somehow didn't manage to post it then.

I know a professor – a youngish white guy who looks older than he is – who wears a suit an tie to every class because, he says, he wants to command authority in the classroom. He doesn’t need to dress up for his students to think he’s the one in charge. All he has to do is feed their assumptions.

I work with another professor who told me during my interview that, as a middle-aged white guy, he knew he could be intimidating, and he’d rather that the subject be the scary part, not him as the instructor. He wears Hawaiian print shirts and makes goofy memes. He makes himself approachable.

And I? I am small and young and female. I want to wear skirts, but I’ve opted for khakis. They’re somehow safer. A friend of mine, who also teaches chemistry, recently told me she had finally “dared” to wear teal tights while teaching. We worry—and I think rightfully so—that if we present as too young and too feminine, that we won’t keep enough of our authority.

I like to be informal with my students. I want them to be comfortable asking questions without fear of looking stupid. But I insist on Dr. Haas. I need to be their professor more than their pal.

—

Since August, three women in gaming have left their homes and changed their speaking plans in response to rape and death threats. Ostensibly this is in a fight over ethics in video game journalism. It’s been reported as a “controversy,” as if there are two equally reasonable sides. But there aren’t two sides here. People are making threats of violence against women. That is wrong. Full. Stop.

In recent years, more and more women in tech & gaming have been targeted simply for being visible. For speaking up. For expressing opinions. For existing in a "male" space.

Science can be a pretty male space, too. Women in science – thankfully – aren't getting the kind of abuse women in gaming are, but that does not mean science is always a welcoming, egalitarian place.

The Nobel prizes in physics and chemistry were announced earlier this month and yet again a bunch of men won the prize, the recognition, the press, the attention, the praise, the legitimacy. There have been two female laureates in physics, and four in chemistry. And that’s not even a total of six women because Marie Curie won both a physics and a chemistry Nobel.

Five women. One hundred years of awards, up to three people each year, and only five women.

Don’t get me wrong. I think the blue LED is wonderful. I’m delighted that my own field, single-molecule microscopy, has been recognized. I think all the men involved are smart and talented and deserving of recognition. I just think we are way past due recognizing women for their works and listening to their voices.

We need to make women more visible. We need to change the norms so that is no longer remarkable to have female scientists or female gamers or female developers or female anything else. When few women stand out, they are seen as anomalies, rareities, and exceptions. Instead of individuals, they become symbols, whether the penultimate female scientist to gather the sisterhood behind or the feminist nail MRAs believe they must hammer down.

—

My heart is full. I am applying for jobs and I doubt myself so strongly sometimes. I worry that my voice will not be heard. That my science will not be recognized. That if I shout into the void, no one will hear, or worse, the darkness will come roaring back at me.

A week or so ago I spent multiple hours trying to write a short reply to a simple email. Sometimes I have opinions that I am afraid to express. I want things I am afraid to ask for. I am so fully aware that men who ask for more are seen more favorably than women who request less. I watch my words like I choose my clothes. Carefully. Weighing consequences. Debating if it’s even worth expressing my preferences, using my voice, making myself more visible.

I know the price of silence. I just worry at times that the price of speaking is greater.

Those who can, do. Those who can explain, teach.

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My mother is an elementary school teacher. She chose that career path at approximately the age of 12 when writing an essay about what she wanted to be when she grew up. And she stuck to it. She's a Master Teacher, an expert in elementary education with extensive experience in remedial reading and math. She's taught nearly every level of elementary school, and since there aren't as many specialized courses in elementary school, she's taught nearly every subject, too.

My brother and I spent many, many Saturday and summer afternoons in my mom's classrooms, or playing in the empty hallways. She teaches in a different district than we went to school in, otherwise I'm sure we'd have spent even more afternoons and evenings at school. I have many memories of stocking bookshelves, cutting out cardstock shapes, keeping an eye on the laminating machine, sorting counters and tools and toys.

From the age of 12, if not before, I was asked "Are you going to be a teacher like your mom?" I got tired of that question very quickly. No, I was not going to be a teacher. Teaching is a lot of work! I didn't want to grade papers and prepare a classroom and write lesson plans. "You'd make a great teacher, just like your mom." Nope. Not doing it.

I went to college with the intent of becoming a science writer. I was a chemistry major on the B.A. track looking to take a lot of writing courses, and possibly double-major with journalism. My academic and research advisors convinced me that if I really wanted to talk about the science, I should learn more of it. So I switched to the B.S. track. And got into research. And fell in love with chemistry all over again.

Graduate school was not originally part of my plan. But after the B.S., it seemed like the logical next step. At that point I wanted a job in industry working on semiconducting materials. A PhD would help that, and I was told it would be much easier to take the "graduate school vow of poverty" before an industry job, rather than after. So I went to graduate school.

The questions about whether I was going to be a teacher then changed a bit. People still asked if I was going to teach, just like mom. But then I'd also get a few "Are you going to be a professor like your grandfather?" Nope. Not teaching. I'm going to be a scientist, not a teacher.

That lasted until about 10 seconds into my first teaching experience as a graduate TA. It turns out that I love teaching. That even when things are hard and crappy and it seems like I don't understand anything at all, I can walk into a classroom and feel alive.

There's a funny thing about being a scientist, though. Even though there's a lot of cultural pressure to be an academic, there's a heaping helping of disdain for anyone who actually wants to teach. You're "supposed" to put research first. Many, many times I would talk to other scientists about future plans and lie right through my teeth. Of course I wanted to go the research path! Of course I wanted a future full of grant-writing and a massive lab of grad students and post-doc!

All I really wanted was a classroom full of curious undergrads and the chance to give them research experience.

This summer, at the Gordon Conference, I was surrounded by R1-types. And I, newly hired for a teaching position, was actually honest about my career goals. I said I wanted to teach undergrads and have the opportunity—but not the requirement—to do research. Some people gave me the "that's nice" dismissal. I had admitted that research was not my #1 Thing. It was like admitting some kind of weakness. Like I am "not a serious scientist" because I care about instruction.

I once had lunch with a seminar speaker who refuses to admit more than one undergrad in her lab at a time, yet seeks out graduate students who, like herself, had undergraduate research experience. She wants to take all of the benefit and share none of the burden. I find that incredibly unfair. But then, I would like to run the sort of lab that feeds graduate programs with experienced undergraduates. I suppose what I want is that burden without the same benefit.

So I plan to teach. And do research. But in that order and not the other way around. That doesn't make me a second-rate scientist. It makes me an educator.

At an institution of higher education, don't you think you need a few educators?

Permission to be here

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One thing that surprised me about the change from grad student to professor is how shy I felt about doing "faculty" things. Checking my department mailbox. Using the copier. Going to meetings.

When I was in high school, I once knocked on the door of the faculty break room during lunch hour, in search of a teacher. Nobody shooed me away, but there was still the feeling that students were verboten from the break room. (And why not? Some of those teachers seriously needed a break from students, if only for a few minutes.)

The first time I went into the Briggs break room I had the same feeling. Like I'd trespassed in Grown-up Land. Except I'm a grown-up too. And I'm a professor too. And I'm totally allowed—even expected—to be there.

I consider how I would feel if there were no other women, or if I were some other minority in the department, or if my college and colleagues were not so supportive. This is how many people do feel, and it's not just in their heads—many workplaces are not welcoming and inviting, people are made to feel uncomfortable and othered. I am lucky that most of what I face is internal. Nobody's actively pushing me out. In fact, they keep welcoming me and encouraging me. They want me to succeed.

I realized I was asking everyone around me for permission to be there, and that was undermining my confidence. I don't need anyone's permission to do my job. I'm the real deal, not an impostor.

Like the spy movie cliché, people tend to assume you belong and you know where you're going. You just have to act like it. Do it long enough, and you might just fool yourself.

So when I feel uncertain now, I just act. I pretend confidence, and the confidence becomes real.

The chemistry Nobel should go to a woman

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It's Nobel Prize season, and everyone has their picks for which chemists might get a phone call from Sweden. All the names I've seen are of accomplished people who've done excellent, influential work. There's a problem with all these lists, though: I haven't seen a single woman on any of them. Not a damn one.1 Also notable: a general lack of brown/black people of either gender. What gives? Chemistry is not solely the domain of white and Asian men.

Folks on Twittter have been passing around the Slate article about the 50-year drought of female laureates in physics, but I think it's worth noting that the story is hardly any better in chemistry. I counted four women among the chemistry Nobel laureates: Marie Curie (1911), Irene Joliot-Curie (1935), Dorothy Hodgkin (1964), and Ada Yonath (2009). Did I miss any? I really hope so. Four is a pitiful number.

Are women really not doing Nobel-worthy work? Or do we not recognize their work with the same prestige?

Do we only recognize the super-women? Those who aren't just better, but leagues better, like Curie and Goeppert-Mayer?

When we speak of scientists, do we remember to count the women? Or do they become faceless and forgotten? Do we even listen when they speak?

So, with a few more hours to go, can we think of a few women who should be on the Nobel shortlist?

Update: I missed C&EN's list, but it also doesn't have any women. Still bummed.

1: Admittedly, I didn't check the much longer list of previous predictions from Everyday Science. I may have overlooked somebody.

Hire me

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I love working at Lyman Briggs, but the job I have is a temporary one. I’m only here for a year. The academic job market has a particular annual cycle, and right now it’s application time for tenure-track positions. This means that though I will be happily teaching chemistry at Briggs from now until May (and possibly into the summer), I have to look for next fall’s job now.

I don’t like applying for stuff. I don’t like selling myself. I worry that nobody will want me, that nobody likes what I do, that I’m not good enough, experienced enough, polished enough to get the job I want. I worry that I’ll be passed over because of my gender, my opinions, my beliefs, my appearance or my personality. I worry that the search for the next job will be a hindrance to the job I am currently doing.

But.

When I can drive the poison of Impostor Syndrome from my addled brain, I remember that I’m actually a competent, qualified instructor with a passion for teaching. I’m an expert in my field, with the publications and fancy diploma to prove it. I am capable and talented and enthusiastic. I have a deep desire to ask and answer scientific questions. I have the potential not just to succeed, but to thrive.

So if you’re at a liberal arts college or regional university and you have an open position in chemistry to fill for next fall, I hope you’ll consider me when my application crosses your desk.

Excited state

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My job has overwhelmed me more times than I can count. I have found it very hard. But I love it. So much. I must be nuts to love this much hard.

So far I’ve had students crying at me in the hallway and at office hours,1 one call to the paramedics, one student at office hours who proceeded to break one of my pens despite several requests to leave it alone, some angry demands for exam points back, some shy requests for office hour help, and many very funny emails.2 I’ve been called Professor a lot, Dr. Haas most of the time, and occasionally mistaken for a student. I’ve been consulted on a medical issue3 and I’ve been thanked for the tiniest things as if I’d bestowed some royal favor.

I’m primarily responsible for a lecture section, but I have to admit that my favorite time is spent in office hours and lab. I love lab. I get to wander through the room, nudging students into understanding. Why did that happen? Did you expect that? What does that mean? Last week’s lab was on light absorption and emission. I stationed myself at the absorption experiment (look at salt solutions with a spectroscope) and peppered the students with questions. Is this absorption, emission, or something else? How do you know?

Last Wednesday, I was going through this with one group, and a young woman got just to the edge of an epiphany—and she started to move. She was practically dancing, moving in place and gesturing as she talked. I could see her eyes light up, and her voice rose as she worked through the questions I hoped would lead to her understanding.

In emission, the electrons are in an excited state and fall to a lower energy state, releasing a photon.

This young woman, shaking with energy, was a student in the excited state. On the verge of enlightenment. It was beautiful.

My Wednesdays are long days. I left home that day around 7 am and got home after 9 pm. And I was finishing an exam, and planning out the next week, and calming test anxieties. Long, long days. It’s hard.

But that dancing student, eyes alight, she made the day sparkle. This is why I love this job.

—

1: I swear they weren’t crying because of me! I don’t want to be the scary professor.

2: Sorry students, but you guys totally crack me up when you’re so very serious.

3: “What should I do about this weird growth?” “Um, take it to a medical doctor? I’m a chemist.”

Blogging silence

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I said blogging would resume, but I haven't posted in weeks. It's not because I haven't been writing. It's just that so many of the words I've written have been sad and angry. And overall I have not been sad and angry. I am delighted with my new job, my wonderful students and my friendly, supportive colleagues. I still have yet to find my balance-point—the last few weeks have not been easy—but I am doing well.

No, the things that have filled the news I read are what creep into my writing: Ferguson, Ebola, war and conflict all over the globe, misogyny nearer to home. So I have written out thoughts and decided not to share them, not to add to the anger and sadness and frustration. I don't want to be yet another angry blogger. I want to contribute in a positive way.

One hard thing about my new job is the time my workday starts. I am not a morning person. At all. I don't get up early easily or happily. I am very good at staying up too late for a good night's sleep, and not so good about dragging myself out of bed the next morning.

My lecture is at 9 am. That would not be much of a struggle, were campus closer, but I drive 65 miles to work. To arrive on time and ready to teach, I get up by 6, which is even earlier than I got up back in high school. It's an incredibly simple thing, getting up early, but so hard for me. To cheer myself—and my students, who may be as grumpy early-risers as I—I start every lecture with a chipper "Good morning" and picture of a sleepy animal. It's silly, but it makes us smile.

We don't start with the serious stuff, the exam worries, the homework frustrations, the mistakes we have made. We start with a smile. A smile's a pretty good way to start the day, I think.

Back from Vacation

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An afternoon in Tuscany

An afternoon in Tuscany

Last month I went to the Single Molecule Approaches to Biology GRC in Italy and had a wonderful time meeting delightful people and learning about cool developments in the field. It was a pretty great week. GRCs don't allow recording of the scientific sessions, but I was allowed to snap a few photos of the gorgeous view from the hotel.

After the conference, my husband and I spent a couple weeks vacationing in Italy and Germany, seeing sights, eating delicious food (we had the best gnocchi in Florence), and visiting old friends of mine. We came home happily tired from all the travel.

After that, I took a sort of technology vacation. It was unintentional to begin with: I had almost gotten used to being Internet-less. But after a few more days, it was really nice not to feel the pressure of email and Facebook and the endless stream of Twitter. That was as relaxing as anything else after we came home.

But I have a new job, and even if it doesn't start until next week, there is preparation to do already. So this week I reconnected myself to the buzzing web. Blogging will resume shortly.

Book Review: Culinary Reactions

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The Book

Culinary Reactions: The Everyday Chemistry of Cooking by Simon Quellen Field

The Premise

This books purports to explain the hows and whys of cooking in terms of the chemistry going on. It's geared toward non-scientists as an "easy-to-follow primer."

The Naming of Things

It was clear to me by page 9 that I am absolutely not the audience for this book. The target audience is not expected to have a scientific vocabulary, so many terms are defined and explained in plain English. Generally I applaud such efforts, but the author's expectations for his readers' vocabulary are inconsistent. For example, he defines homogeneous versus heterogeneous mixtures and but doesn't explain what he means by "conjugated" molecules. Anyone who has every purchased homogenized milk could probably take a stab at a working definition of homogeneous, but conjugated? No way.1 Here's another example (p. 51):

It is viscoelastic like toothpaste, meaning it can liquefy under shear stress and be pumped or extruded easily.

I doubt my non-scientist relatives would be familiar with shear stress and extrusion, even when compared to toothpaste.

The Power of an Editor

I'm not sure if the author had an editor. If he did, that person needed to be more heavy-handed with the red pen. The entire book is a disorganized jumble. There is no flow from chapter to chapter. There doesn't even seem to be much logic to the order of the chapters. Chapter 1 is on measuring and weighing; take a guess what Chapter 2 is.

Heat? No. Acids and bases? No. Nutrition? No. Proteins, fats and sugars? No, no, no.

Chapter is on foams. Heating, meanwhile, is Chapter 11.

I suspect that this book is a reformatted collection of blog posts, but that doesn't excuse the unfocused and meandering writing. (For one thing, The Joy of x was also a collection of blog posts and it was far more coherent than this book.) The disorganization is even reflected in the structure of the chapters themselves, and even individual paragraphs. For example, this is the first paragraph in the Oxidation of Oils and Fats section of Chapter 13 (Oxidation and Reduction, p. 211):

Oils and fats react with oxygen in ways. That are sometimes beneficial and sometimes undesirable. When cooking oils react with oxygen, they can form compounds that taste bad; they're rancid. But when oils react with oxygen and polymerize into rough insoluble films, they're used in paints and coatings for wood products.

Yum! Paint and wood coating! Gosh, I'm glad he included that in a book on food chemistry. It was totally necessary to include that random fact in the main text of the chapter. /sarcasm

Other paragraphs amount to laundry lists of facts. Lists are fine, but when he claims to explain why and how the chemistry works, saying "it works in A, it works in B, it works in C, it works in D“ doesn't answer why or how. When I consider that not a single fact is backed up – no references, no lists of further reading, not even the names of the people who did the research or the institutions where the work was done – I get cranky. Good science writing tells you where you can go to find more of the details. This book doesn't do that.

Bad Science

And now we get to the real kicker: a bunch of the chemistry in this book is just plan wrong. I could overlook a lot of faults if the science were solid, but it's not, and the parts that I know are wrong make me doubt the whole rest of the book. There were several points when I went "That's pretty cool…if it's true." Without references, I can't know if his sources were bad or his understanding is weak. (I suspect both.) And I'll need to do my own search to find out if those cool-if-true statements have any grounding in scientific fact.

Here's one example of bad chemistry (p. 99):

Since carbon dioxide is a gas, there are no bonds holding it together that have to be broken before it can dissolve [into water].

I read that sentence to two chemist friends and thoroughly enjoyed watching their eyes pop out of their faces and their jaws hit the floor.

The Bottom Line

Don't read this book. It's not worth it. If you're looking for a book on the science of food, stick with the classic On Food and Cooking: The Science and Lore of the Kitchen by Harold McGee1 or read Alton Brown's cookbooks, which are mostly good at explaining the science. This book just does not measure up and threatens instead to undermine facts with misconceptions.

The Silver Lining

You might ask – as my husband did every time I exclaimed "What?!" while reading – why did I bother finishing the book if I found it so awful? Simple: it could be an excellent teaching tool. There are several examples in this book of chemistry misconceptions that my students may have. Not only can I use these as prompts for my own explanations, I am itching to give one or two of these to my students to have them explain what's wrong.

Okay, the 'carbon dioxide is a gas and has no bonds' statement is crap, but why is it crap? How do we know that it's wrong – and what experiments could we do to test it? What misunderstanding of chemistry underlies the statement? How can we change the sentence to get the chemistry right?

By the end of freshman chemistry, my students need to have a thorough enough understanding that hearing such statements makes their eyes bug-out too.

1: Early in grad school, I heard a physicist give a presentation (to a group of chemists) in which she began explaining conjugation. We (the chemists) told her the explanation wasn't necessary; we were pretty familiar with the term. She said something like "how come you all know this?" But conjugation is a major concept in organic chemistry, which we had all taken and she had not. It was a good reminder to me not to take discipline-specific knowledge for granted.

All of that is to say that if a physics PhD candidate doesn't think of "conjugation" as an everyday term, you can bet that a random science Muggle off the street will have no idea what it means.

2: I admit, I haven't finished On Food and Cooking yet, but as far along as I am, I can assure you the science is more sound than in Culinary Reactions.

Book Review: The Joy of x

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Joy of x.jpg

The Book

The Joy of x: A Guided Tour of Math, from One to Infinity, by Steven Strogatz

The Premise

Steven Strogatz, a mathematics professor at Cornell, had a math blog (On the Elements of Math) at the New York Times for a while in 2010. This is a collection of those blog posts edited into book form.

Fun with math

I read On the Elements of Math when it was new. The topics were varied and interesting,and the writing was clear. It was equally fun to review things I knew (e.g. explaining the Pythagorean theorem by drawing squares on the triangle's sides) and learn about things I hadn't encountered before (e.g. the Hilbert Hotel problem). I enjoyed it and was sorry to see it come to an end.

It has been a few years since then, and I had forgotten the specifics of the blog when I picked up The Joy of x. (It was kind of interesting just to see which parts I recalled versus what felt like new material.) The topics are still interesting, the stories are still chosen well, and the writing is still clear. I think I enjoyed the first few chapters again as much as I had when I'd read them in blog-post form.

But by the fourth or fifth chapter, my enthusiasm started to lag.

The chapters were starting to sound the same. They had essentially the same structure: identify a potential limitation of math, relate anecdote or pop culture reference, explain the problem in the story, end with a punch line. The chapters are short, so it's easy to run through the pattern several times in one sitting, and it gets repetitive quickly.

I set the book aside and read something else. When I did pick it up again, I read only a chapter at a time and found it much improved. It was like returning to the blog: only one post at a time and a break between one and the next. It's a funny way for me to read a book,1 but it worked.

The Bottom Line

It's a fun survey of mathematics by someone who obviously loves the subject. No math expertise is necessary to follow along. Read it a bit at a time, like it was originally delivered.

1: I'm a devourer, a binge-reader. I have been known to read lengthy series in a week or weekend and I read the final Harry Potter book in a single sitting the night I bought it. Reading a book in little bites is not like me.

More on career breaks

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I have a few more things to say about how taking a break from science/academia could kill a woman's career.

First, the Executive Director of the Elsevier Foundation wrote a letter to the New York Times about retaining women in STEM (emphasis mine):

The work-life balance challenge faced by working women is particularly difficult for those in STEM professions (science, technology, engineering and math). Taking time off the research track can be a potentially career-ending decision for a woman, as she can lose valuable connections and funding.

Career brakes indeed. This letter prompted me to flip the issue and think about it from another side: what if men took more career breaks? The anecdata I have say that paternity leave (or, parental leave, in more generic terms) is becoming more common. Could we make it an expectation that parents will take breaks?

I have heard of a university (but now can't seem to find the article in which I read about it) that stops the tenure clock for new parents automatically. They have to ask for it not to stop, rather than the other way around. This is to encourage people to use the parental leave they have and make using it less stigmatized. It's a simple enough policy that might actually change academic culture. Parental leave is generally a few months, not multiple years, of course, but if we can change the attitudes about short breaks, I think it's possible to make longer breaks more acceptable, too.

Then there's this post at Chronicle Vitae about the proliferation of "quit lit," the genre of essays about leaving academia. I have read a number of quit lit pieces, but what strikes me about the topic this time around is that academia is a place people leave. Not take a break from, but leave for good. In that sense, it's not just women who might be unwelcome to return after time away, though men aren't likely to be accused of "leaning out" in the process.

I have to wonder how much of this attitude is related to the priesthood of science (and academia in general) and the ridiculous notion that "dedicated" scientists are single-minded in the pursuit of their work to the exclusion of other interests or obligations. I'm not sure and have no data to back it up, but I suspect they are linked.

Lastly, here are a few thoughts about working parents, moms in particular.

From an interview with Indra Nooyi, CEO of PepsiCo.:

I don't think women can have it all. I just don't think so. We pretend we have it all. We pretend we can have it all. My husband and I have been married for 34 years. And we have two daughters. And every day you have to make a decision about whether you are going to be a wife or a mother, in fact many times during the day you have to make those decisions. And you have to co-opt a lot of people to help you. We co-opted our families to help us. We plan our lives meticulously so we can be decent parents. But if you ask our daughters, I'm not sure they will say that I've been a good mom. I'm not sure. And I try all kinds of coping mechanisms.

She says "you have to make a decision about whether you are going to be a wife or a mother," but is her husband also presented with the same decisions about being a husband or a father? Maybe, but maybe not.

I also feel the need to invoke the Finkbeiner test on her interviewer, even though she's not a scientist.1 Until men are asked in equal proportion about how they balance family with work, we have got to stop interrogating women about it.

Finally, go read this post by dinahere about being the daughter of a working mother.

For the first 12 years of my life I don’t remember my father being there for my birthdays or attending a school play. He was busy saving lives in the OR, earning his share of the money and my mother was there for all of those occasions. So, why didn’t his absence count while hers did? Why were her absences so glaring while her presence so fading?

You know why. Women will never be able to have it all because what we think ‘all’ refers to has been pre-determined by a society that will always be stacked against us.

We can't keep blaming women when they don't measure up to an unachievable standard. The culture has got to change.

1: I'll just leave this right here, in case you haven't seen it yet.

What's next

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I defended my thesis in April, and turned in my dissertation at the end of May, but I haven't left my grad lab yet. Here's what I've been up to, and what's coming up next.

Wrapping up

First I'm wrapping up some things. I've been revising and polishing two papers (one is done and submitted, the other will follow shortly), doing a few experiments for my last project, and getting things ready to hand off to the next person.

Most of my dissertation work was about watching the motions of one protein, TcpP, that is involved in the pathway for producing cholera toxin in Vibrio cholerae. Cholera toxin is the compound (a protein complex) that makes you so very sick if you contract cholera. TcpP (along with another protein, ToxR) activates the transcription1 of the toxT gene. The ToxT protein activates transcription of the cholera toxin genes.

Aside from its role in cholera toxin production, TcpP is interesting because it (and ToxR, too) is bound to the inner membrane of the bacterium. In order to activate transcription, TcpP and ToxR must bind to the DNA, but somehow they manage to do this without leaving the membrane. Since DNA tends to be compacted into the center of the cell2, it's pretty remarkable that two proteins on the membrane can find a specific region of DNA and bind to it. There aren't many proteins that bind DNA while bound to a cellular membrane, but there are a few besides these two.

To learn more about TcpP and how it pulls off this trick, we labeled it with a fluorescent protein and watched it move around the cell. My part of this project is done. Another grad student will watch ToxR move around to learn more about how these two proteins interact. So I'm updating my index of data files, checking that any protocols I've revised are up to date, and commenting the Matlab code I've written that he might use for analysis.

My other dissertation project was a collaboration with my labmate Jess, who has been studying fluorescence enhancement by plasmonic surfaces. I've been learning about plasmon-enhanced fluorescence for years, and it still seems a little bit sci-fi to me: by shining light on metal nanoparticles, you can create an enhanced electric field that makes fluorescent molecules shine brighter and longer.3 Jess has been enhancing fluorescent proteins using nano-structured gold surfaces. A while back we began pairing my fluorescently labeled bacteria with her plasmonic surfaces, to see if we can get enhancement inside live cells. We had some success [$] with our initial experiments, and the project has grown from there. Just because my dissertation is done doesn't mean this project is, though. I've been busy with experiments and trouble-shooting throughout June, and Jess will carry it on after I leave.

Shipping out

My last week as a Biteen lab member will not be spent in lab, but at the Single-Molecule Approaches to Biology Gordon Research Conference in Italy. I like the GRC conference style, and I can't wait to hear all the latest and greatest research in the field. It doesn't hurt that the conference is at a resort in Tuscany, either.

After the conference, it's time for vacation. My husband will meet me in Italy, and we'll tour parts of Italy and Germany and visit some friends of mine from my time as an exchange student. Then it's back to the States so my husband can get back to work and I can enjoy a couple of weeks of unemployment (and prepare for the next job).

Moving on

Mid-August I start my new job. For the next year, I will be a visiting instructor at Lyman Briggs College at Michigan State. (Yes, I'm going to be an adjunct.) I'm excited to move to Briggs: the program is interesting, the faculty I've met have all been delightful people, and this job feels like the right thing for me right now.4 Briggs students take science classes that emphasize active learning, and "HPS" courses (history, philosophy and sociology of science) that give them context for science in their lives. As I said to several people while interviewing, Briggs is the kind of place I'd have loved to attend as an undergrad. I'm delighted to teach there. It's gonna be great.

1: transcription: just like you can talk about transcribing text, i.e. copying words from one place to another, we talk about transcribing genes: copying nucleic acid "words." The nucleic acids are slightly different—DNA is copied into RNA—but both kinds of nucleic acid "words" are the instructions for building proteins.

The process of decoding RNA to protein parts is called "translation." Again, it's just like text, translating from one language (e.g. French, or, in the case of genes, nucleic acids) to another (e.g. English or, for proteins, amino acids). Stitch those translated words together, and you get functional sentences (or proteins!).

2: In eukaryotic cells, such as your own human cells, DNA is stored in the cell nucleus. Bacteria don't have nuclei, but they still keep their DNA kind of bundled up in the middle.

3: It's more complicated than that, but that's the general idea.

4: It's a one-year position, and that suits me fine. My long-term goal is still to get a tenure-track position or a permanent position off the tenure path—I want more certainty in my employment than adjuncting is likely to supply. For the next year, though, I'm very happy to teach at Briggs.

A one-year appointment also means I will go through the whole job application process again this fall. Yay

Career brakes

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From SciLogs:

When Adam Spencer asked if female scientists should consider taking an extended break of two or three years, the answer was a resounding “No.” “Science is really a fast-moving world,” [Suzanne] Cory said. “If you get out, even for three years, it becomes very difficult to get back in.

I have heard that position many times from both men and women, and I find it repugnant. It’s a “that’s the way it is” kind of attitude.

My grandmother was a music teacher before she was a mother. She’s told me if she could do it again, she would have become an accountant, but that’s not something girls did in those days. Girls could become teachers, nurses or secretaries. And then they could become mothers. Boys could become accountants or scientists or doctors or lawyers or whatever else they wanted. “That’s the way it is.”

Well that’s not the way it is now, and thank goodness. Thank goodness that somebody stepped up and said “This is what I want to do, and my gender doesn’t matter.” Thank goodness for the women who took the hard path – and the men who helped them – so that I could become a scientist. So that I could be treated as an equal.

Does my expertise have an expiration date? Does leaving the lab for more than a month make me forget how to be a scientist? Will my PhD turn into a pumpkin after midnight? No.

But “science is a fast-moving world” they insist. So what? We all had to learn how to get into that world once, so why can’t someone do it a second time? People also change fields and get into new topics they haven’t studied before. How is that any different from “getting into” the world of science after time away? No, the “fast-moving” argument strikes me as justification to leave things as they are and not bother to make it better.

It galls me to think that women are told that if they leaves, they will not be welcome back—that a career break soon becomes a career brake.

The panel in the article was discussing “possible solutions to fixing this leaky pipeline.” Their conclusion appears to be that women shouldn’t leave in the first place.1 But why on earth don’t we do something to support the women who want to come back?

1: Suzanne Cory:

“You are at a crucial age now. Don’t drop off.”

The panelists also said that women need more confidence. Tell me just how much confidence I’ll have after I’ve been told time and again that it’s damn hard to be a woman in science and you can’t leave because then you’ll have let down Womanhood and leaked out of the pipeline, and if you do go you won’t be welcome back because Reasons. And how far will that confidence get me when my words are ignored until spoken by a man? How confident do I need to be to get men to stop patting me on my head? How much confidence will I need to muster to get a seat at the table and be able to keep it?

I have sworn off Women in Science luncheons because I’m sick being told that the solution for the leaky pipeline is “Believe in yourself,” like if I just close my eyes and click my heels together, that will just fix everything.

MATLAB Tip of the Day: Counting in the Command Window

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This is actually a two-fer: padding a number with a variable number of leading zeros or spaces and updating text in the Command Window without creating a bunch of new lines.

Variable number padding

The sprintf function includes in its documentation the instructions for padding a number with leading zeros.

myNumber = 4
paddedNumber = sprintf('%02d', myNumber)

paddedNumber =
        04

But what do you do when you don't know how many zeros you'll want to use? You need another variable. The syntax looks like this:

paddedNumber = sprintf('%0*d', numDigits, myNumber)

If I specify numDigits, I can pad myNumber with any number of zeros I choose. Of course, I need to define numDigits somehow. In the FrameCounter function below, I want to have enough leading zeros that my last frame has no zeros out front. So if my last frame is 123, I should get two leading zeros for numbers less than 10, one leading zero for numbers up to 99, and then no leading zeros for the rest. Here's how I like to do it:

numDigits = length(sprintf('d', lastNumber));

This is to say, I write out the number as a string and calculate how many characters that is (i.e. the length of the string). That's how many digits I need to do the padding. Simple.

Updating text in the Command Window

I was using a program in MATLAB that took a long time to run and had an unfortunate tendency to crash1. I wanted to know which frame it had been working on before it failed, and in general I wanted to have some idea how much progress it had made. At the time, I wasn't aware of the built-in progress bar, and then I learned that that can actually slow down whatever process it is you're trying to keep tabs on, so I wrote my own. It just printed the current frame number to the Command Window every ten frames or so, which was enough to narrow down the range of the failed frame. Every time a new frame was printed to the Command Window, though, it made a new line, and after thousands of successful frames, I had a Command Window full of numbers. What I wanted was a way to update the number in place, without printing a new line.

In 2011, I went to the CPLC Summer School at UIUC (which was pretty fun and enlightening) and I saw what I wanted in action in an analysis program. I didn't have a chance to look at the source, though, so I asked how it worked. The student I was working with said he didn't recall for sure, but he thought it had something to do with backspaces. That clue was enough for me to figure it out on my own.

Here's how it works:

  1. Print the text you want to display to the Command Window using fprintf.
  2. Print enough backspace characters (again, with fprintf) to delete each of the characters that need to change.
  3. Print the new text.

Getting it to work as a separate function took a little thinking, but turned out to be pretty simple. The result is below. I hope you find it (or its components) as useful as I have over the years.

FrameCounter

function FrameCounter(first_num, last_num, current_num, show_text)
%%  Determine the number of digits in the number
num_digits = length(sprintf('%d',last_num));
text = 'Frame ';
if nargin < 4
    show_text = 0;
end
%%  Before displaying the first number
if current_num == first_num
    if show_text == 1
        %%
        % Display "Frame " before the numbers
        fprintf(text)
    end
    for aaa = 1:num_digits
        %% Prime the counter with spaces
        fprintf(' ')
    end
end
%% Remove the previous number
for bbb = 1:num_digits
    fprintf('\b')
end
%%  Display the current number
fprintf('%0*d', num_digits, current_num)
%%  Last number
if current_num == last_num
    if show_text == 1
        char_num = length(sprintf(text));
    else %if show_text == 0
        char_num = 0;
    end
    backspaces = char_num + num_digits;
    pause(.1) % Without this pause, the last number sometimes doesn't display properly.
    %% Remove last number and "Frame " text
    for ccc = 1:backspaces
        fprintf('\b')
    end
end
end

1: The source of the crash was a read/write conflict with the Windows 7 indexing system. More on that conflict here if you're interested.

The best scientist I know

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Joe Palca asked me on Twitter this morning,1

Who is the best scientist you know, and what qualities make her/him the best?

I had to think a moment about this. I'm sure many people who love science have a favorite historical scientist. My shortlist is mostly crystallographers: Kathleen Lonsdale, Dorothy Crowfoot Hodgkin, the Braggs (Sr. and Jr.), Linus Pauling,2 and I am amused by the story of Alessandro Volta, who was such a great practitioner of the scientific method, that he felt the need to zap himself with his electro-motive apparatus over and over again on various parts of the body "where the skin is very delicate" to make sure it really worked.3

Who is the best scientist you know? It's a simple enough question, but it can be interpreted in several ways. For one, what sense of "know" are we considering?

  • Who is the best scientist you know of?
  • Who is the best scientist you have seen (at a conference, seminar, etc.)?
  • Who is the best scientist you have met?
  • Who is the best scientist who knows your name in return?
  • Who is the best scientist you know personally?

Then we should consider what we mean by "best scientist"? The follow-up question (what qualities…?) allows us to define our own criteria for best, but who gets to be a scientist? Must we consider only professional scientists?

Because this question has so many variations, I have several answers. Here are two scientists I aspire to be more like.

W.E. Moerner is one of the best scientists I know. I have heard him speak on a few occasions, and I have read a fair number of his papers. My advisor was a postdoctoral fellow in his laboratory, and from comments she has made over the course of my PhD, I believe that experience has significantly influenced her approach to science and advising.

Dr. Moerner gave a seminar at UM once, and I was among the students and post-docs who ate lunch with him. We had sandwiches and chips in the Biophysics conference room, and he chatted with each and all of us about a variety of topics. Someone asked him about his work with Kador on single-molecule spectroscopy, and he jumped up to the white board and started sketching out diagrams and explaining the story. He did so clearly and carefully, and seemed to have all the patience in the world when someone didn't understand. He has a reputation for being brilliant, and that made me a bit intimidated at first, but that feeling wore off quickly. He was approachable and just plain excited to tell us about the neat things he'd learned. And he didn't just talk to us, he conversed with us.

Krishanthi Karunatilaka is one of the best scientists I know personally. She was a post-doc in our lab until last fall. She is absolutely meticulous; I have some real notebook-envy for her tidy, organized notes in clear and even handwriting. She is driven and dedicated without any of the pushiness that I have come to associate with those terms. She has worked some long, hard days because she wants to know the answers to the questions she has. She also finds balance. I know that her Saturday mornings in Ann Arbor were set aside for a peaceful cup of coffee on her apartment balcony. She doesn't get knocked down by failures. If an experiment doesn't work (or gives unexpected answers), she has another idea, she keeps rolling on. When someone else is struggling, she's the first person to say "Don't worry, you can try something else. Keep going." She has a talent for presenting even brand-new data in a way that makes it sound like she's considered their implications for weeks.

Other names come to mind as well,4 but you'd find they follow the same pattern: the best scientists I know do good, thoughtful, careful scientific work, and are also excellent teachers, communicators, and just generally nice people.

So those are my "best scientists." Who are the best scientists you know? What makes them the best?

1: I admit, I had a complete fan-girl moment.

2: I admire Marie Curie, too, but she is used so often as The Token Female Scientist, that I think of the words of Mr. Bennet: “That will do extremely well… You have delighted us long enough. Let the other young ladies have time to exhibit.”

3: From Volta's letter to the Royal Society:

If, by means of an ample contact of the hand (well moistened) I establish on one side a good communication with one of the extremities of my electro-motive apparatus … and on the other I apply the forehead, eye-lid, tip of the nose, also well moistened, or any other part of the body where the skin is very delicate: if I apply, I say, with a little pressure, any one of these delicate parts, well moistened, to the point of a metallic wire, communicating properly with the other extremity of the said apparatus, I experience, at the moment that the conducting circle is completed, at the place of the skin touched, and a little beyond it, a blow and a prick, which suddenly passes, and is repeated as many times as the circle is interrupted and restored.

4: For example, my introduction to Jenny Glusker was similar in many respects to my lunch with Dr. Moerner.

Victor DiRita, a collaborator and dissertation committee member of mine, is another one of the best scientists I know. He teaches me something every time time we meet, even if only for a few minutes.

The best amateur scientist I know is probably my uncle Tom, for lots of the same reasons. He is also the only person I know who gets really excited about moss.

Swift

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I got an iPod Touch in 20091 and wished from the start that I could write my own apps for it.2 I knew approximately nothing about coding, though, so it was a rather far-away sort of wish.

In grad school I learned to code in Matlab. It was a sink-or-swim kind of thing. With the help of another grad student, two books, the wonders of Matlab Central (and later StackExchange), and lots of practice, I learned how to write and debug programs.

My brother is a programmer, and by his standards I'm a hobbyist at best, but I can make the computer do what I need, and I've gotten better as I've gone. Still, he teases me about how I should learn a "real" language, and I kind of agree. So about a year ago, after listening to a Mac Power Users episode about learning to code, I bought a book about learning Objective-C.3 I got a little better than halfway through it before other things got in the way; it's one of the things I was planning to come back to this summer between grad school and job.4

Those summer plans may have just changed, though. A week or two ago at the WWDC Keynote, Apple announced a new programming language called Swift and I think I'm in love. I watched the demo and thought "I can definitely do this." I may finally be able to write the apps I wished for. There's an eBook about the language, which I've already started reading. Though it starts from "Hello world," I don't think it would be much help if you had no familiarity with programming whatsoever,5 but it does look promising for someone (like me) who has at least dipped their toes into the programming pool before.

So that's my next side project: learn another language, try to make an app (I have several ideas), and see how it goes. I'm excited to get started.

1: Nearly 5 years later, it's a bit sluggish but still kicking.

2: I was also bowled over by the idea that the device playing podcasts in my pocket had a bigger hard drive than my laptop's original drive: 64 vs 60 GB. When I stop to think about it, it still amazes me how powerful the gadgets in my pockets and bags are. And then I start feeling old…

3: It's a really good book, too: The Big Nerd Ranch Guide. My inability to finish it has much more to do with being an overwhelmed graduate student in need of "off" time for my brain than the quality of the book. I highly recommend it, and I think it's an excellent example of instructional writing.

4: Oh yeah, I accepted a job about the same time I was completely overloaded with dissertation and defense stuff. The defense is done, the dissertation is submitted, and though I wrote about the stresses and thrills of job-hunting, I guess never did mention here that I did accept an offer. More on that another time. Short version: I have a job starting in August and I'm excited about it!

5: This is actually the same gripe I have about the Matlab Getting Started Guide and books for "beginners." All of these say that you can start from scratch, but they usually assume knowledge and vocabulary that a first-time programmer may not have. (I'm looking at you, floating-point array.)

Consider these programming languages like human languages: the Getting Started Guide might tell me how a verb is conjugated, but if I don't know what "conjugation" is, I don't know what to do with that information. If you've learned another language before, you've probably learned the meta-terminology already, and have some kind of structure for understanding this new set of words, sounds, and grammar rules.